don't know. Can you send the recon-all.log file? doug On 05/25/2015 07:13 PM, Anvi K Vora wrote: > Hi Doug, > > That file does not exist, because none of the surf files got created > from this pipeline. So there was an error before that? > > The mri files got created (partially) and what's there looks good. > Missing are: aseg.mgz, aparc.a2009s+aseg.mgz, aparc+aseg.mgz, > aseg.auto.noCCseg.mgz, aseg.auto.mgz, brain.mgz, brain.finalsurfs.mgz, > lh.ribbon.mgz, rh.ribbon.mgz, filled.mgz, wm.mgz, wm.seg.mgz > > There is plenty of memory here on the server. But is this maybe an > issue with job timing out of server? Otherwise memory and space not an > issue. > > Any help appreciated. Thank you, > Anvi > > > On May 25, 2015, at 6:38 PM, Douglas Greve <gr...@nmr.mgh.harvard.edu > <mailto:gr...@nmr.mgh.harvard.edu>> wrote: > >> >> The error says: >> >> mris_fix_topology: could not read input surface >> /sc/orga/projects/psychimage/MCIC/Schizophrenia/SiteC/Cooked/A00036129/Freesurfer/A00036129/surf/lh.qsphere.nofix >> No such file or directory >> >> Does that file exist? Have you run out of disc space on that volume? >> >> doug >> >> >> On 5/22/15 8:11 PM, anvi vora wrote: >>> Hello, >>> >>> So recon-all seems to be running on my Mac fine, with this same >>> data. But it does not run on my institution's Minerva linux server. >>> >>> It did most of volumetric processing steps, but failed on surface >>> processing steps, and then all of the rest. >>> >>> I have checked that environment variables are correct, and they are >>> I believe. >>> >>> Attached is the entire recon-all.log file >>> >>> I will appreciate any help! >>> >>> Thank you very much, >>> Anvi >>> >>> >>> >>> >>> _______________________________________________ >>> Freesurfer mailing list >>> Freesurfer@nmr.mgh.harvard.edu >>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> >> The information in this e-mail is intended only for the person to >> whom it is >> addressed. If you believe this e-mail was sent to you in error and >> the e-mail >> contains patient information, please contact the Partners Compliance >> HelpLine at >> http://www.partners.org/complianceline . If the e-mail was sent to >> you in error >> but does not contain patient information, please contact the sender >> and properly >> dispose of the e-mail. > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
-- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
